EIC cut or not shown for some or samples in DIA

EIC cut or not shown for some or samples in DIA dennisjakob  2022-09-07 07:40

Hi support team,
I am working on an isotope tracing experiment where we used a DIA method on a Bruker Impact II instrument to record the data.
In general I am very satisfied on how skyline handles the data but I have a problem with some ion traces.
For example sample QC-pool_2: I have two Isomers listed in the Molecule List "MGDG". One traces for the second Isomer is shown, for the first it is not. Also, and this occurs for multiple molecules and samples, the ion trace is shorten on both sides. You can also see this in the example of MGDG and sample QC-pool_2.

I uploaded the skyline document with the name 'MS012_share.sky' to the share folder. Attached you find a screenshot from Bruker DA with the EIC of the MGDG and the raw data file of QC-pool_2 in case you need to reimport this particular sample.

I hope you have an idea what is wrong here.


Nick Shulman responded:  2022-09-07 08:38
If you extract chromatograms from both MS2 and MS1, and Skyline notices that MS2 chromatograms cover a shorter time range than the MS1, Skyline will truncate the MS1 chromatograms so they cover the same time range as the MS2.
The reason that Skyline does this is that it is the correct thing to do if you have a schedules MS2 method where you have told the mass spectrometer when to collect MS2 spectra for specific molecules.

One thing that you can do to prevent Skyline from doing this is to tell Skyline that your MS2 acquisition method is "DDA". You can set the Acquisition Method at "Settings > Transition Settings > Full Scan".
When the acquisition method is "DDA", Skyline will not truncate your MS1 chromatograms. Also, Skyline will treat all of your MS2 peak areas as "non-quantitative" and the MS2 chromatograms will be drawn as dotted lines on the chromatogram graph.

I was not able to open the .d file that you attached (SeeMS.exe give me the error "Important blocks missing from main BAF file.") When I look at the chromatograms in your Skyline document, it looks like they might have come from DDA, since those MS2 chromatograms have long straight lines indicating periods of time when the mass spectrometer did not acquire a MS2 spectrum which matched the precursor.
-- Nick